*
* @return
*/
- public ViewportRanges getRanges();
+ ViewportRanges getRanges();
/**
* calculate the height for visible annotation, revalidating bounds where
*
* @return total height of annotation
*/
- public int calcPanelHeight();
+ int calcPanelHeight();
/**
* Answers true if the viewport has at least one column selected
boolean isNormaliseSequenceLogo();
+ boolean isShowInformationHistogram();
+
+ boolean isShowHMMSequenceLogo();
+
+ boolean isNormaliseHMMSequenceLogo();
+
ColourSchemeI getGlobalColourScheme();
/**
boolean isIgnoreGapsConsensus();
+ boolean isIgnoreBelowBackground();
+
boolean isCalculationInProgress(AlignmentAnnotation alignmentAnnotation);
AlignmentAnnotation getAlignmentQualityAnnot();
*
* @return
*/
- AlignCalcManagerI getCalcManager();
+ AlignCalcManagerI2 getCalcManager();
/**
* get the percentage gaps allowed in a conservation calculation
*/
void setFollowHighlight(boolean b);
+ /**
+ * configure the feature renderer with predefined feature settings
+ *
+ * @param featureSettings
+ */
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
+ * Apply the given feature settings on top of existing feature settings.
+ */
+ public void mergeFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+ /**
* check if current selection group is defined on the view, or is simply a
* temporary group.
*
@Override
void setProteinFontAsCdna(boolean b);
- TreeModel getCurrentTree();
+ void setHmmProfiles(ProfilesI info);
+
+ ProfilesI getHmmProfiles();
+
+ /**
+ * Registers and starts a worker thread to calculate Information Content
+ * annotation, if it is not already registered
+ *
+ * @param ap
+ */
+ void initInformationWorker(AlignmentViewPanel ap);
+
+ boolean isInfoLetterHeight();
- void setCurrentTree(TreeModel tree);
+ public abstract TreeModel getCurrentTree();
/**
* Answers a data bean containing data for export as configured by the
*/
AlignmentExportData getAlignExportData(AlignExportSettingsI options);
+ public abstract void setCurrentTree(TreeModel tree);
+
/**
* @param update
* - set the flag for updating structures on next repaint